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<h1>Methodology<br>
</h1>
<h2>Introduction</h2>
This program uses distance geometry [<a href="References.htm#Blaney1994">Blaney1994</a>,<a
 href="References.htm#Crippen1981">Crippen1981</a>] to do pharmacophore
searches and to generate a set of molecular conformations that match a
pharmacophore. The matching conformations are "cleaned up" using a
molecular
force field [<a href="References.htm#Rappe1992">Rappe1992</a>,
<a href="References.htm#Casewit1992">Casewit1992</a>] and aligned to
the reference pharmacophore.<br>
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The general algorithm for finding matching conformations for a probe
molecule is:<br>
<ol>
  <li><a href="BuildingBoundsMatrix.htm">Build the distance bounds
matrix</a> for the probe</li>
  <li><a href="FindingMappings.htm">Find all mappings</a> of the
pharmacophore's feature types onto the probe</li>
  <li><a href="MatchingPharmacophores.htm">Find all compatible mappings</a>
by searching through the mappings to find those where the probe's
bounds matrix is compatible with the pharmacophore's distance
requirements<br>
  </li>
  <li><a href="GeneratingStructures.htm">Generate molecular conformations</a>
for each compatible mapping, "clean up" the resulting conformations
using a force field, then align those conformations to the reference
pharmacophore.<br>
  </li>
  <li><a href="ScoringAlignments.htm">Score the generated alignments</a>
using several metrics.<br>
  </li>
</ol>
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